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-   -   Mapping and base calling (http://seqanswers.com/forums/showthread.php?t=12164)

atgc 06-18-2011 09:13 PM

Mapping and base calling
 
Hello,

I recently received sequencing data from Illumina's HiSeq. The reads are 100 bp, paired end. The data has been provided to us in fastq format.

I have worked with PE sequencing earlier. However, initially, data was provided in a txt format which we imported into CLC Genomics Workbench. Does anyone know if the fastq format can be imported into CLC Genomics Workbench?
Thanks for your help in advance.

ATGC

sklages 06-19-2011 03:38 AM

Just works like importing the qseq files (what you probably did import before as txt). Select to import fastq.

atgc 06-19-2011 09:45 AM

Thank you.

boetsie 06-19-2011 02:54 PM

First of all; probably the 'older' .txt format was also a .fastQ format. CASAVA spits out a .txt file, which is basically a .fastQ file.

Anyway; Best way to import Illumina Paired-end data is to go to 'File -> Import High-throughput sequencing data -> Illumina". Select here both paired-reads and choose your file format (.fastQ). See this link from CLC:
http://www.clcbio.com/index.php?id=1..._Illumina.html

Illumina HiSeq data can be treated the same as Illumina Genome Analyzer data.

atgc 06-19-2011 08:57 PM

Initially the paired end read data that was given to me was two files/ sample - a forward and a reverse read. However this new data set includes 4 or more files / sample. I don't understand why this is.

sklages 06-19-2011 11:06 PM

Quote:

Originally Posted by atgc (Post 44485)
Initially the paired end read data that was given to me was two files/ sample - a forward and a reverse read. However this new data set includes 4 or more files / sample. I don't understand why this is.

If this data has been generated via CASAVA 1.8 then this is due to the fact that every fastq file generated has a constant number of sequences (except for the last one which holds the remainder), but at most 16mio. So one lane of HiSeq data is almost always splitted into more than one read (fastq) file.

E.g.
Code:

sample2_CGATGT_L003_R1_001.fastq.gz
sample2_CGATGT_L003_R2_001.fastq.gz
sample2_CGATGT_L003_R1_002.fastq.gz
sample2_CGATGT_L003_R2_002.fastq.gz
sample2_CGATGT_L003_R1_003.fastq.gz
sample2_CGATGT_L003_R2_003.fastq.gz

hth, Sven

atgc 06-20-2011 12:10 PM

That helps. Thanks.

atgc 06-20-2011 01:24 PM

I am getting an error when I import fastq reads into the CLC Genomics Workbench.

The message reads as follows:

"The data seems to be corrupt or originates from different sources since the input files contain different number of reads. The previous sequences have been properly saved but it is highly likely the import data is incomplete or defective. Please double-check the sources."

I have two forward and two reverse fastq files. I tried to import only one of each and I still get the error when importing.

Would anyone here know the source of this error or what it means.

Thanks for your help in advance.


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